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Error while running "make_fragments.pl".....[blastpgp] ERROR: Arguments must start with '-'

hello

I am encountering errors while trying to make fragments locally by using the script "make_fragments.pl". The command which I am using is

perl make_fragments.pl -verbose -nosam -noporter 1elwA.fasta

but it gives error

VERBOSE.
don't run porter.
don't run sam.
FILENAME: 1elwA.fasta
no id specified. parse filename instead.
INTERMEDIATE: 1elwA.fasta
ID: 1elw CHAIN: A
Sequence: EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR

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ddg_monomer.mpi

ddg_monomer doesn't seem to work well with mpi. I would like it to send it a job with a large amount of mutation combinations and use the mpi enabled version to finish the job quickly.

Consider the following protocol:
mpirun -np 4 /rosetta3.3/rosetta_source/bin/ddg_monomer.mpi.linuxgccrelease @ddg.flag -in:file:s min_cst_0.5.input.pdb -constraints::cst_file ca.ca.dist.cst -ddg::mut_file example.mut -ddg::iterations 50

#example.mut is a simple mutation, for instance a Leu to Ala mutation on res 1
total 1
1
L 1 A

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Ligand Docking Positive Control: wt ligand

Hi Everyone!

I'm Ben, I'm new here. I'm working on re-designing the binding pocket of an amino-acid binding protein for it to bind a new ligand. For this, I use enzdes. I want to compare the designs Rosetta makes with the wt protein in terms of binding energy (i.e. ligand-protein surface interaction energy) as a control. My question is: Is ligand docking the right application for this?

My plan in detail:

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∆G calculation script for protein and mutation of AA at each residue

Hello all,

I am working on a script that takes a given cleaned (using the cleaning.py script) pdb file (attached as dG_calc.txt) that mutates each residue through the sequence of amino acids and calculates the dG and ddG. This is based on the ala_scan.py script except no docking or other things.

I had a couple of questions:

1) Does the mutate_residue in PyRosetta 2.0 repack the side chains automatically? If so to what distance?

2) If not, does PackRotamersMover take care of this? If I need to use this I should restrict the packer so it only uses the original amino acids?

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How to relax a protein model calling Rosetta functions from my C++ code

My code creates protein models that need to be relaxed in order to lower their energy as these models may have some close contacts and other non-protein like features. According to the online documentation, the Rosetta command for relaxing non-idealized structures is
rosetta.exe aa xxx_ -relax -farlx -minimize -s xxx.start -fa_input -fa_output -use_input_bond

My questions are: 1) Is this the correct command for relaxing my models and make them "fall" in the nearest local minimum? 2) If so, how can I call these functions from inside my C++ code?

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Error while running Enzyme Design

Hello,
I am attempting to use the Enzyme Design application to redesign a ligand binding site to accept a different ligand. I am running the following command:

$ROSETTA33/bin/enzyme_design.linuxgccrelease -database $ROSETTA33/rosetta_database -in:file:s input.pdb -in:file:extra_res_fa LG2.cen.params LG2.fa.params LG1.cen.params LG1.fa.params -enzdes:cstfile constraints.cst -enzdes:detect_design_interface -enzdes:cst_design

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Selecting Top Scoring Decoys

Hi

I have a silent file of 20,000 decoys and I want to extract/separate low energy decoys out to a separate silent file for all atom relax. Is there any possibility of doing it. I tried cluster.linuxgccrelease with -cluster:output_score_filter and it doesn't seem to work! Is there any workaround or possibilities of any script!

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